SNTA1 (syntrophin alpha 1)

Gene

• Entrez ID: 6640
• Gene name: Syntrophin alpha 1
• Gene symbol: SNTA1
• Synonyms (NCBI Gene): LQT12, SNT1, TACIP1, dJ1187J4.5
• Chromosome: 20
• Chromosome location: 20q11.21
• Summary: Syntrophins are cytoplasmic peripheral membrane scaffold proteins that are components of the dystrophin-associated protein complex. This gene is a member of the syntrophin gene family and encodes the most common syntrophin isoform found in cardiac tissues

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs56157422	G>A,C,T	Conflicting-interpretations-of-pathogenicity, uncertain-significance, likely-benign	Coding sequence variant, missense variant
rs121434500	G>A	Likely-pathogenic, pathogenic	Coding sequence variant, missense variant
rs139532210	C>G,T	Conflicting-interpretations-of-pathogenicity, uncertain-significance, likely-benign, benign	Intron variant
rs141724500	G>A,T	Conflicting-interpretations-of-pathogenicity, uncertain-significance, likely-benign	Coding sequence variant, missense variant
rs144860423	G>A	Conflicting-interpretations-of-pathogenicity, uncertain-significance, likely-benign	Missense variant, coding sequence variant
rs572545726	G>A	Benign, likely-benign, conflicting-interpretations-of-pathogenicity	Genic upstream transcript variant, coding sequence variant, missense variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT022575	hsa-miR-124-3p	Microarray	18668037

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0002027	Process	Regulation of heart rate	IMP	18591664
GO:0003779	Function	Actin binding	IEA
GO:0005198	Function	Structural molecule activity	IEA
GO:0005515	Function	Protein binding	IPI	9356463, 10212242, 16192269, 16533813, 18468998, 19931615, 26617989, 27382054, 28514442, 33961781
GO:0005516	Function	Calmodulin binding	IEA
GO:0005737	Component	Cytoplasm	IEA
GO:0005856	Component	Cytoskeleton	IEA
GO:0005886	Component	Plasma membrane	IEA
GO:0005886	Component	Plasma membrane	TAS
GO:0006936	Process	Muscle contraction	TAS	8576247
GO:0016010	Component	Dystrophin-associated glycoprotein complex	IBA
GO:0016013	Component	Syntrophin complex	TAS	21164104
GO:0016020	Component	Membrane	IEA
GO:0016328	Component	Lateral plasma membrane	TAS	21164104
GO:0017080	Function	Sodium channel regulator activity	IBA
GO:0017080	Function	Sodium channel regulator activity	IMP	18591664
GO:0030165	Function	PDZ domain binding	IEA
GO:0031594	Component	Neuromuscular junction	IBA
GO:0031594	Component	Neuromuscular junction	IEA
GO:0032991	Component	Protein-containing complex	IDA	18591664
GO:0042383	Component	Sarcolemma	IBA
GO:0042383	Component	Sarcolemma	IEA
GO:0044325	Function	Transmembrane transporter binding	IPI	18591664
GO:0050998	Function	Nitric-oxide synthase binding	IPI	18591664
GO:0051117	Function	ATPase binding	IPI	18591664
GO:0060307	Process	Regulation of ventricular cardiac muscle cell membrane repolarization	IMP	18591664
GO:0070161	Component	Anchoring junction	IEA
GO:0086005	Process	Ventricular cardiac muscle cell action potential	IBA
GO:0086005	Process	Ventricular cardiac muscle cell action potential	IMP	18591664
GO:1902305	Process	Regulation of sodium ion transmembrane transport	IMP	18591664

Other IDs

• MIM: 601017
• HGNC: 11167
• e!Ensembl: ENSG00000101400

Protein

• UniProt ID: Q13424
• Protein name: Alpha-1-syntrophin (59 kDa dystrophin-associated protein A1 acidic component 1) (Pro-TGF-alpha cytoplasmic domain-interacting protein 1) (TACIP1) (Syntrophin-1)
• Protein function: Adapter protein that binds to and probably organizes the subcellular localization of a variety of membrane proteins. May link various receptors to the actin cytoskeleton and the extracellular matrix via the dystrophin glycoprotein complex. Plays
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF00595	PDZ	87 → 167	PDZ domain	Domain
  PF18012	PH_17	208 → 266	PH domain	Domain
  PF00169	PH	294 → 401	PH domain	Domain

• Tissue specificity: TISSUE SPECIFICITY: High expression in skeletal muscle and heart. Low expression in brain, pancreas, liver, kidney and lung. Not detected in placenta.
• Sequence:

  MASGRRAPRTGLLELRAGAGSGAGGERWQRVLLSLAEDVLTVSPADGDPGPEPGAPREQE
  PAQLNGAAEPGAGPPQLPEALLLQRRRVTVRKADAGGLGISIKGGRENKMPILISKIFKG
  LAADQTEALFVGDAILSVNGEDLSSATHDEAVQVLKKTGKEVVLEVKYMKDVSPYFKNST
  GGTSVGWDSPPASPLQRQPSSPGPTPRNFSEAKHMSLKMAYVSKRCTPNDPEPRYLEICS
  ADGQDTLFLRAKDEASARSWATAIQAQVNTLTPRVKDELQALLAATSTAGSQDIKQIGWL
  TEQLPSGGTAPTLALLTEKELLLYLSLPETREALSRPARTAPLIATRLVHSGPSKGSVPY
  DAELSFALRTGTRHGVDTHLFSVESPQELAAWTRQLVDGCHRAAEGVQEVSTACTWNGRP
  CSLSVHIDKGFTLWAAEPGAARAVLLRQPFEKLQMSSDDGASLLFLDFGGAEGEIQLDLH
  SCPKTIVFIIHSFLSAKVTRLGLLA

• Sequence length: 505

Pathways

KEGG:

Cytoskeleton in muscle cells
Hypertrophic cardiomyopathy
Arrhythmogenic right ventricular cardiomyopathy
Dilated cardiomyopathy
Viral myocarditis

Associated diseases

Evidence Score:

• ★☆☆☆☆  Gene-disease association found in Text Mining only
• ★★☆☆☆  Found in Text Mining and Unknown/Other Associations
• ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources
• ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants)
• ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
Atrial fibrillation	Conflicting classifications of pathogenicity	ClinVar Disgenet	★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
BASAL CELL CARCINOMA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Becker muscular dystrophy	Conflicting classifications of pathogenicity	ClinVar Disgenet	★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
BREAST CARCINOMA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Brugada syndrome	Conflicting classifications of pathogenicity	ClinVar Disgenet	★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
CANCER	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cardiovascular phenotype	Conflicting classifications of pathogenicity; Uncertain significance; Likely benign; Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
COLORECTAL CANCER	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Congenital long QT syndrome	Conflicting classifications of pathogenicity; Uncertain significance; Benign; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Dilated cardiomyopathy 3B	Conflicting classifications of pathogenicity	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DMD-ASSOCIATED DILATED CARDIOMYOPATHY	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Duchenne muscular dystrophy	Conflicting classifications of pathogenicity	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ESTROGEN-RECEPTOR NEGATIVE BREAST CANCER	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
FAMILIAL LONG QT SYNDROME	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Long QT syndrome	Conflicting classifications of pathogenicity; Likely benign; Uncertain significance; Benign	ClinVar ClinGen, Disgenet ClinGen, Disgenet	★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
Long QT syndrome 1	Conflicting classifications of pathogenicity; Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Long QT syndrome 12	Conflicting classifications of pathogenicity; Uncertain significance; Benign; Likely benign	ClinVar CTD, ClinVar, Disgenet, GenCC, HPO CTD, ClinVar, Disgenet, GenCC, HPO CTD, ClinVar, Disgenet, GenCC, HPO CTD, ClinVar, Disgenet, GenCC, HPO	★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
Long QT syndrome 2	Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
LUNG ADENOCARCINOMA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
LUNG CARCINOMA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MELANOMA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MYELOPROLIFERATIVE DISORDER	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
NON-MELANOMA SKIN CARCINOMA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
OVARIAN CARCINOMA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
OVARIAN ENDOMETRIOID CARCINOMA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
OVARIAN SEROUS CARCINOMA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Primary dilated cardiomyopathy	Benign; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PROSTATE CARCINOMA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ROMANO-WARD SYNDROME	—	Disgenet, Orphanet Disgenet, Orphanet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Sick sinus syndrome	Uncertain significance	ClinVar Disgenet	★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
SNTA1-related disorder	Likely benign; Conflicting classifications of pathogenicity; Benign; Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SQUAMOUS CELL LUNG CARCINOMA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
STATUS EPILEPTICUS	—	CTD, Disgenet CTD, Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Thyroid cancer, nonmedullary, 1	Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Ventricular fibrillation	Uncertain significance	ClinVar Disgenet	★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
VENTRICULAR FIBRILLATION, PAROXYSMAL FAMILIAL, 1	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Ventricular fibrillation, paroxysmal familial, type 1	Conflicting classifications of pathogenicity	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Ventricular tachycardia	Conflicting classifications of pathogenicity	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Wolff-Parkinson-White pattern	Conflicting classifications of pathogenicity	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
WOLFF-PARKINSON-WHITE SYNDROME	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Arrhythmias Cardiac	Cardiac arrhythmias	Pubtator	35762211	Inhibit	★☆☆☆☆ Found in Text Mining only
Arrhythmias Cardiac	Cardiac arrhythmias	Pubtator	35773684	Associate	★☆☆☆☆ Found in Text Mining only
Atrial Fibrillation	Atrial Fibrillation	BEFREE	29714131		★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
Atrial Fibrillation	Atrial Fibrillation	CLINVAR_DG			★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
Breast Carcinoma	Breast Carcinoma	BEFREE	16682955, 24434436		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Breast Neoplasms	Breast neoplasm	Pubtator	24434436	Associate	★☆☆☆☆ Found in Text Mining only
Cardiomyopathies	Cardiomyopathy	Pubtator	35773684	Associate	★☆☆☆☆ Found in Text Mining only
Cardiomyopathy Hypertrophic	Hypertrophic cardiomyopathy	Pubtator	35773684	Associate	★☆☆☆☆ Found in Text Mining only
Complex Partial Status Epilepticus	Status Epilepticus	CTD_human_DG	20886625		★☆☆☆☆ Found in Text Mining only
Congenital long QT syndrome	Congenital Long QT Syndrome	BEFREE	18591664		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Dementia	Dementia	BEFREE	30120299		★☆☆☆☆ Found in Text Mining only
Dementia	Dementia	Pubtator	30120299	Associate	★☆☆☆☆ Found in Text Mining only
Dysautonomia	Dysautonomia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Grand Mal Status Epilepticus	Grand Mal Status Epilepticus	CTD_human_DG	20886625		★☆☆☆☆ Found in Text Mining only
Hypertrophic Cardiomyopathy	Hypertrophic cardiomyopathy	BEFREE	21430528		★☆☆☆☆ Found in Text Mining only
Keratoconus	Keratoconus	Pubtator	31467338	Associate	★☆☆☆☆ Found in Text Mining only
Long QT Syndrome	Long QT Syndrome	BEFREE	19684871, 20009079, 20920651, 23376825, 27028743, 31529317		★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
Long QT Syndrome	Long qt syndrome	Pubtator	20809527, 23376825, 36528013	Associate	★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
Long QT Syndrome	Long QT Syndrome	CLINVAR_DG			★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
Long Qt Syndrome 12	Long QT Syndrome	GENOMICS_ENGLAND_DG	16301704, 19684871		★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
Long Qt Syndrome 12	Long QT Syndrome	UNIPROT_DG	18591664, 19684871		★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
Long Qt Syndrome 12	Long QT Syndrome	CTD_human_DG			★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
Long Qt Syndrome 12	Long QT Syndrome	CLINVAR_DG			★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
Malignant neoplasm of breast	Breast Cancer	BEFREE	16682955, 24434436		★☆☆☆☆ Found in Text Mining only
Malignant Neoplasms	Malignant Neoplasm	BEFREE	24434436		★☆☆☆☆ Found in Text Mining only
Muscular Dystrophy Duchenne	Duchenne muscular dystrophy	Pubtator	23426965	Associate	★☆☆☆☆ Found in Text Mining only
Muscular Dystrophy, Duchenne	Duchenne Muscular Dystrophy	BEFREE	23426965		★☆☆☆☆ Found in Text Mining only
Narcolepsy type 1	Narcolepsy	BEFREE	29449194		★☆☆☆☆ Found in Text Mining only
Narcolepsy-Cataplexy Syndrome	Narcolepsy-Cataplexy Syndrome	BEFREE	29449194		★☆☆☆☆ Found in Text Mining only
Non-Convulsive Status Epilepticus	Nonconvulsive status epilepticus	CTD_human_DG	20886625		★☆☆☆☆ Found in Text Mining only
Parkinson Disease	Parkinson disease	Pubtator	34092653	Associate	★☆☆☆☆ Found in Text Mining only
Petit mal status	Petit Mal Status	CTD_human_DG	20886625		★☆☆☆☆ Found in Text Mining only
Presenile dementia	Senile Dementia	BEFREE	30120299		★☆☆☆☆ Found in Text Mining only
Romano-Ward syndrome	Romano-Ward Syndrome	Orphanet			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Romano-Ward Syndrome	Romano-Ward Syndrome	ORPHANET_DG	24093767		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Short Qt Syndrome	Short QT Syndrome	BEFREE	29874177		★☆☆☆☆ Found in Text Mining only
Status Epilepticus	Status Epilepticus	CTD_human_DG	20886625		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Status Epilepticus, Subclinical	Status Epilepticus	CTD_human_DG	20886625		★☆☆☆☆ Found in Text Mining only
Torsades de Pointes	Torsades de Pointes	HPO_DG			★☆☆☆☆ Found in Text Mining only
Ventricular Fibrillation	Ventricular Fibrillation	HPO_DG			★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)